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Questions tagged [upsetr]

58 questions
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R package for intersection visualisation

I am looking for a R package that I can use to generate such a figure (see image below). intersection tree I found it in an article but I did not find any mention on how they created such a plot. It remind me the second part of an Upset diagram but…
Coddy
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R ggplot ggupset - Create inset with combinations that have fewer intersection

I am looking for a way to subset my input data so I can make a second upsetR plot that shows the resolution of the sample intersections that are <<100 (for example). As an example, I'm using the tidy_movies data from tidyverse and the ggupset…
shu251
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Is there a R function to add the count of horizontal bars beside the bars in UpSetR plot?

I used the upset(fromList(x), show.numbers = 'yes', order.by = 'freq') query to plot the UpSetR plot. But it is showing only the count of vertical bars on the top of vertical bars. I want the count of horizontal bars too. If there is a command to…
amu
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Error in upset_data : unused argument (nsets = 5) What could be causing this and how coul I fix the issue?

I am very new to R and I would like to make UpSet plot of peptides. I have five lists (sets) in .txt format (ID_list_vysledok_pos_vs_healthy_files.txt, ID_list_vysledok_pos_neg_files.txt, ID_list_vysledok_New_vs_Old_collumn_files.txt,…
adam urminský
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Loop for UpSet plots

I have a number of data frames I would like to create UpSet Plots for in R and write them to an external folder. I am using similar code that I am successfully using to create and save scatterplots to an external folder. Below are two example data…
chipsin
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UpsetR - choosing intersections to visualize

I would like to use Upset plot instead of venn diagram to show overlap between specific groups (20 in total). However, one of the group (number 10) is the most important for me and I would like to present how many unique values is in that specific…
Shaxi Liver
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Error creating ggplot/ggupset from list-column

I am trying to create a ggplot from a list column. First I create the list column and then the ggplot. The intended ggplot is a ggupset to show set intersections. I followed the ggupset example to create the list column and plot. However, I get the…
maia-sh
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Using upset R for survey data visualization?

I am able to use to generate basic and attribute upset plots using the UpsetR package. But, I am not able to generate plots using survey data. Has anyone tried making upset plots in survey data? Thanks. My error is: "cannot coerce class…
Laxmi
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R Convert categorical data to dummy set by other variable

I have this data set, I put a screenshot of real data instead of a code or something. sorry for messing up, I am a newbie here in R enter image description here Then, I want to change the data into dummy set for "13 Source" categorical data, but it…
Gugi Yogaswara
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How to fix "Error in `$<-.data.frame`(`*tmp*`, "x", value = 1L) : replacement has 1 row, data has 0" when using upsetR?

Below a simulated data which will be an input to upset() function nobs <- 4000 pb <- round(runif(n=1, min=0.1, max=0.8),1) August <- rbinom(n=nobs, size=1, prob=pb) pb <- round(runif(n=1, min=0.1, max=0.8),1) September <- rbinom(n=nobs, size=1,…
Afiq Johari
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UpSetR colSums(data[sets]) : 'x' must be numeric

I have a scRNA-seq dataset and I am trying to plot the coexpression frequency of 4 genes and I decided to do this with UpSetR, However I am getting an error and I do not know how to fix it. I have my dataframe as an .RDS file and this is how it…
AvolaAMG
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